Thaps_bicluster_0245 Residual: 0.28
Thalassiosira pseudonana

Module Page Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.
Title Residual Model version Organism
Thaps_bicluster_0245 0.28 Thalassiosira pseudonana
Displaying 1 - 20 of 20
10055 hypothetical protein

10055 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10055
11779 hypothetical protein

11779 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11779
20664 hypothetical protein

20664 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20664
21371 AdoMet_MTases superfamily

21371 - AdoMet_MTases superfamily

GO Terms:

GO:0003824

CD Domains:

Go To Gene Page:

21371
22526 ABC_MTABC3_MDL1_MDL2

22526 - ABC_MTABC3_MDL1_MDL2

GO Terms:

GO:0005524, GO:0006810, GO:0016021, GO:0042626, GO:0016887, GO:0000166, GO:0017111, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

22526
23651 hypothetical protein

23651 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23651
2575 RIO superfamily

2575 - RIO superfamily

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

2575
262271 PIP5K

262271 - PIP5K

GO Terms:

GO:0016308, GO:0004431

CD Domains:

Go To Gene Page:

262271
263848 Voltage_gated_ClC superfamily

263848 - Voltage_gated_ClC superfamily

GO Terms:

GO:0005247, GO:0006821, GO:0016020

CD Domains:

Go To Gene Page:

263848
31785 not_thiJ

31785 - not_thiJ

GO Terms:

NA

CD Domains:

Go To Gene Page:

31785
37662 ATPase-IIA1_Ca

37662 - ATPase-IIA1_Ca

GO Terms:

GO:0005524, GO:0006812, GO:0015662, GO:0016020, GO:0005388, GO:0006816, GO:0016021, GO:0003824, GO:0008152, GO:0016820

CD Domains:

Go To Gene Page:

37662
38647 REC

38647 - REC

GO Terms:

GO:0000156, GO:0000160, GO:0003677, GO:0006355

CD Domains:

Go To Gene Page:

38647
40232 (OAM1) Glyco_hydro_47 superfamily

40232 - (OAM1) Glyco_hydro_47 superfamily

GO Terms:

GO:0004571, GO:0005509, GO:0006487, GO:0016020

CD Domains:

Go To Gene Page:

40232
40713 SodA

40713 - SodA

GO Terms:

GO:0004784, GO:0006801, GO:0046872, GO:0004785, GO:0008382, GO:0008383, GO:0016954

CD Domains:

Go To Gene Page:

40713
4502 hypothetical protein

4502 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4502
6693 hypothetical protein

6693 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6693
7506 Uba3_RUB

7506 - Uba3_RUB

GO Terms:

GO:0004839, GO:0006464, GO:0006512, GO:0003824, GO:0004842

CD Domains:

Go To Gene Page:

7506
8303 Glyco_trans_1_2

8303 - Glyco_trans_1_2

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412

CD Domains:

Go To Gene Page:

8303
9388 hypothetical protein

9388 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9388
9880 SGNH_hydrolase superfamily

9880 - SGNH_hydrolase superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

9880
GO ID Go Term p-value q-value Cluster
GO:0006821 chloride transport 0.00495611 1 Thaps_bicluster_0245
GO:0006801 superoxide metabolism 0.00988969 1 Thaps_bicluster_0245
GO:0006487 N-linked glycosylation 0.0123481 1 Thaps_bicluster_0245
GO:0006816 calcium ion transport 0.0148008 1 Thaps_bicluster_0245
GO:0000160 two-component signal transduction system (phosphorelay) 0.0650367 1 Thaps_bicluster_0245
GO:0006512 ubiquitin cycle 0.0858385 1 Thaps_bicluster_0245
GO:0006812 cation transport 0.101723 1 Thaps_bicluster_0245
GO:0006464 protein modification 0.137086 1 Thaps_bicluster_0245
GO:0006412 protein biosynthesis 0.342653 1 Thaps_bicluster_0245
GO:0006810 transport 0.372449 1 Thaps_bicluster_0245
Log in to post comments